HEADER HYDROLASE 14-DEC-07 2VJW TITLE CRYSTAL STRUCTURE OF THE SECOND GAF DOMAIN OF DEVS FROM TITLE 2 MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAF FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 232-380; COMPND 5 SYNONYM: GAF-B; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: 232-373 OF DEVS PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 1772; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGST-PARALLEL1 KEYWDS GAF, HISTIDINE KINASE, HYPOXIA SENSING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.S.KANG,H.Y.CHO,H.J.CHO REVDAT 3 24-FEB-09 2VJW 1 VERSN REVDAT 2 14-OCT-08 2VJW 1 JRNL REVDAT 1 26-AUG-08 2VJW 0 JRNL AUTH J.M.LEE,H.Y.CHO,H.J.CHO,I.J.KO,S.W.PARK,H.S.BAIK, JRNL AUTH 2 J.H.OH,C.Y.EOM,Y.M.KIM,B.S.KANG,J.I.OH JRNL TITL O2- AND NO-SENSING MECHANISM THROUGH THE DEVSR JRNL TITL 2 TWO- COMPONENT SYSTEM IN MYCOBACTERIUM SMEGMATIS. JRNL REF J.BACTERIOL. V. 190 6795 2008 JRNL REFN ISSN 0021-9193 JRNL PMID 18708494 JRNL DOI 10.1128/JB.00401-08 REMARK 2 REMARK 2 RESOLUTION. 2.0 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 9590 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 485 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 688 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 964 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.184 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.166 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1005 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1373 ; 1.273 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 136 ;16.080 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 39 ;33.192 ;24.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 148 ;15.432 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;20.463 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 169 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 763 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 450 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 715 ; 0.296 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 42 ; 0.132 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 19 ; 0.212 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.163 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 686 ; 0.785 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1092 ; 1.425 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 319 ; 1.843 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 281 ; 2.892 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2VJW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-07. REMARK 100 THE PDBE ID CODE IS EBI-34755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 294 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000 REMARK 200 DATA SCALING SOFTWARE : HKL2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10102 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 40.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.2 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.70 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.5 REMARK 200 R MERGE FOR SHELL (I) : 0.38 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.5 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.18067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.36133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.27100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.45167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.09033 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 261 REMARK 465 ASP A 262 REMARK 465 ALA A 263 REMARK 465 SER A 264 REMARK 465 GLU A 374 REMARK 465 LEU A 375 REMARK 465 ASP A 376 REMARK 465 ILE A 377 REMARK 465 LEU A 378 REMARK 465 ALA A 379 REMARK 465 ASP A 380 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VKS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GAF-B DOMAIN OF DEVS REMARK 900 FROM MYCOBACTERIUM SMEGMATIS DBREF 2VJW A 232 380 UNP A0R2U9 A0R2U9_MYCS2 232 380 SEQRES 1 A 149 ASP PRO ALA THR VAL PHE ARG LEU VAL ALA ALA GLU ALA SEQRES 2 A 149 LEU THR LEU THR GLY ALA ASP GLY THR LEU VAL ALA VAL SEQRES 3 A 149 PRO ALA ASP PRO ASP ALA SER ALA ALA GLU GLU LEU VAL SEQRES 4 A 149 ILE VAL GLU VAL ALA GLY ALA VAL PRO ALA GLU VAL GLU SEQRES 5 A 149 ALA SER ALA ILE PRO VAL GLN ASP ASN ALA ILE GLY GLN SEQRES 6 A 149 ALA PHE ARG ASP ARG ALA PRO ARG ARG LEU ASP VAL LEU SEQRES 7 A 149 ASP GLY PRO GLY LEU GLY GLY PRO ALA LEU VAL LEU PRO SEQRES 8 A 149 LEU ARG ALA THR ASP THR VAL ALA GLY VAL LEU VAL ALA SEQRES 9 A 149 VAL GLN GLY SER GLY ALA ARG PRO PHE THR ALA GLU GLN SEQRES 10 A 149 LEU GLU MSE MSE THR GLY PHE ALA ASP GLN ALA ALA VAL SEQRES 11 A 149 ALA TRP GLN LEU ALA SER SER GLN ARG ARG MSE SER GLU SEQRES 12 A 149 LEU ASP ILE LEU ALA ASP MODRES 2VJW MSE A 351 MET SELENOMETHIONINE MODRES 2VJW MSE A 352 MET SELENOMETHIONINE MODRES 2VJW MSE A 372 MET SELENOMETHIONINE HET MSE A 351 12 HET MSE A 352 8 HET MSE A 372 8 HETNAM MSE SELENOMETHIONINE FORMUL 2 MSE 3(C5 H11 N O2 SE) FORMUL 3 HOH *41(H2 O1) HELIX 1 1 PRO A 233 GLY A 249 1 17 HELIX 2 2 PRO A 279 GLU A 283 5 5 HELIX 3 3 ASN A 292 ARG A 301 1 10 HELIX 4 4 THR A 345 MSE A 372 1 28 SHEET 1 AA 6 ALA A 286 PRO A 288 0 SHEET 2 AA 6 GLU A 268 GLY A 276 -1 O LEU A 269 N ILE A 287 SHEET 3 AA 6 GLY A 252 PRO A 258 -1 O THR A 253 N ALA A 275 SHEET 4 AA 6 THR A 328 GLY A 338 -1 O VAL A 332 N ALA A 256 SHEET 5 AA 6 GLY A 315 ALA A 325 -1 N GLY A 316 O GLN A 337 SHEET 6 AA 6 ARG A 304 LEU A 306 -1 O ARG A 304 N VAL A 320 LINK C GLU A 350 N MSE A 351 1555 1555 1.33 LINK C MSE A 351 N MSE A 352 1555 1555 1.32 LINK C MSE A 352 N THR A 353 1555 1555 1.33 LINK C ARG A 371 N MSE A 372 1555 1555 1.33 LINK C MSE A 372 N SER A 373 1555 1555 1.33 CISPEP 1 GLY A 311 PRO A 312 0 2.32 CRYST1 73.232 73.232 48.542 90.00 90.00 120.00 P 61 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013655 0.007884 0.000000 0.00000 SCALE2 0.000000 0.015768 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020601 0.00000